At Olivia's apartment, Peter gets a call from the cleaning lady at the Liberty Island souvenir shop, saying that she saw Olivia disappear, and that Olivia gave her a message that she's trapped in the other universe. When Bolivia asks who it was, he dismisses it as a telemarketing call. She goes to sleep and Peter lies awake for a couple of hours. He finally gets up and starts going through Bolivia's belongings and finds the photos they had taken together.
Peter then checks her laptop computer and finds an encrypted file. Before he can try to open it, Bolivia comes in and asks what he's doing. Peter says he's talking to a friend in Greece, and quotes her the line in Greece, "Be a better man than your father," that Olivia told him when she returned from the Other Side. She gives him a syringe to inject and then asks if he's going to come after her. Peter promises that he'll kill her if he finds out she harmed Olivia, and then injects himself with the paralytic.
Bolivia goes to the antique store and gets the key from the owner.
The next morning, Walter and Broyles find Peter and the medics revive him. Broyles traces the call and confirms that it was sent from a Manhattan phone booth. Peter insists that they have to get to the Other Side to rescue Olivia, but Walter warns that there's no safe way that he knows of. When Broyles asks why Peter was where he was in the early morning, Walter tries to cover for his son, but Peter admits he's been involved with Bolivia. Peter then realizes that Bolivia took the wrong computer.
At the store, the owner complains that Bolivia's people haven't kept their promise to him in the last seven years. When Bolivia checks the laptop computer, she realizes that she took the wrong one.
The Other Side
Brandon meets with Walternate and says that he'll need to make an exchange to get their Bolivia back. Walternate tells him to use Olivia, and Brandon asks for permission to perform several invasive surgeries, while making sure to keep her at equivalent mass. Colonel Broyles then comes in as Brandon leaves, and Walternate explains that they are close to ensuring the safety of their world. He informs Broyles that Bolivia will soon be returning, and they propose a toast to her safe return.
As Broyles leaves, he sees Olivia being taken away. She begs him for help but he keeps on going.
Peter and Astrid go to the lab and discover that Bolivia had Olivia's debriefing files, and used them to impersonate her. Broyles arrives and tells that Bolivia stole one of Walternate's recovered weapon pieces. Walter, eating one of the cookies that Bolivia brought him, complains that she used her wiles to trick him and Peter alike, and Astrid realizes that Bolivia got the food from the same Bronx bakery every time. They go to check out the area around the bakery.
Bolivia receives a message from her superiors. Once she reads it, she tells the owner he has to do one more thing to get his legs back, and gives him a metal box.
Peter, Walter, and Broyles arrive at the pastry shop. They split up to search the area, and Peter visits the antique shop. He shows the owner a photo of Bolivia, but the owner claims not to have seen her. Peter looks around and finds his computer. He brings in Walter and Broyles and they examine the typewriter. Walter realizes it can be used to communicate across universes, and Peter discovers an imprint on the ribbon referring to Penn Station in Newark.
The Other Side
Colonel Broyles goes to a bar to get a drink, and the bartender says that he's a hero and doesn't need to pay. He goes back to Liberty Island and comes to see Olivia, and says that his son is doing better thanks to her. Olivia begs him to help her get to the lab so she can go home, and explains that they plan to cut out her brain and study it, and then put it back before sending her back in return for Bolivia. Broyles wonders why he should help her when the two worlds are at war, but Olivia insists that the breaches were triggered by Walter coming to get Peter, and she came to save him. When Broyles wonders if he can risk trusting her, Olivia says that if he can't trust her, then there's no hope. An orderly comes in and starts to prepare Olivia for surgery, and Broyles leaves.
Broyles takes his wife Diana to an arboretum in Central Park, and she asks what's on his mind. He finally says that he has to decide, and reminds her of the dimensional breaches. However, to fix them, they'll have to go to war, and billions will die. Broyles isn't sure if he can live with that, and there is an alternative. He wonders if he can play God with other people's lives, and Diana assures him that she knows he can do it, and they need to restore hope to the world.
As Broyles, Peter, and Walter drive to Penn Station, Walter admits that he doesn't have any ideas. Broyles assures an uncertain Peter that if anyone is strong enough to get back, it's Olivia.
The Other Side
Brandon prepares to operate on a paralyzed Olivia. As he prepares to cut into her spine, Broyles comes in, knocks Brandon out, and frees Olivia. He realizes that she's paralyzed and gives her adrenaline to undo the effects. They get to the elevator and head for the ground floor lab so she can use the sensory deprivation tank.
Brandon's assistant returns and finds Brandon, unconscious.
Olivia finds bags of Cortexiphan, and realizes that Walternate has uncovered the secret to crossing over. As she realizes that the tank is empty and she can't cross over, the alarms go off. She tells Broyles to leave her and then explains that she'll swim to shore and get to Walternate's lab in Boston. Olivia figures that he had a sensory deprivation tank there, just as Walter does, and she can use that to cross over. Broyles warns that they've changed the harbor patrols and she'll never make it, and takes her with him.
Walternate gets word that Olivia has escaped from Liberty Island.
Bolivia arrives at Penn Station, enjoys a last cup of coffee, and waits. Her male shapeshifter contact from the Other Side arrives and tells her that it's time to come home. He takes her to the restroom and gives her an injection, and explains that he's had eight identities in the last eight years.
Peter and the others arrive and confirm that the police have sealed the building. Broyles gives Peter a gun and Walter insists that he doesn't need one. They go inside and split up.
As he gives her an injection into her spine, the shapeshifter tells Bolivia that she has 23 minutes until the transfer at 4:00. A woman comes in and is shocked when she sees what they're doing.
Peter comes by the restroom and sees Bolivia and the shapeshifter emerge. He shoots at them and they duck back inside. Broyles and his men surround the restroom, but Bolivia comes out, holding the woman hostage. The woman's daughter runs up and calls to her mother, and Peter realizes that the male shapeshifter hasn't shown himself. He asks the mother what her daughter's name is. When "she" doesn't respond, he shoots her in the forehead, revealing it's a shapeshfiter. The authorities take Bolivia into custody. As she's taken away, she tells Peter that he started off as just an assignment, but came to mean something more. He doesn't believe her and they take her away. A policeman finds Bolivia's bag, and Peter finds the photos of him and her together inside.
The Other Side
Olivia and Broyles go to Walternate's lab and find his old sensory deprivation tank. They fill it with water and salt, and Broyles prepares to give her a Cortexiphan injection. The soldiers arrive outside and Broyles realizes they used his subcutaneous tracker to follow him. He tells her to make it worth it and gets her into the tank. Olivia tries to relax as the soldiers realize where she is and tries to open the tank.
Astrid is working in the lab when she turns and sees Olivia emerge from the tank. Olivia smiles... and then collapses.
As Broyles prepares Bolivia for transport, he gets a phone call. Meanwhile, Walter examines the injection components, small metal spines, and says they look familiar. As the clock strikes 4, Bolivia's hands start to glow red at the injection sites. Walter hears the metal spines vibrating, and then listens as Broyles tells Peter that Olivia has arrived at the lab. However, she's had a seizure and they took her to Boston General. Before Peter can go, Walter explains that the spines are similar to the ones he and Bell used to cross objects between worlds. The neighborhood shakes and they run to the van. Peter opens the door and then warns Broyles back: an Olivia-sized mass of the alternate Broyles has transitioned, dead.
The Other Side
Bolivia arrives at Fringe Headquarters and smiles in triumph. Lincoln greets her and notes that he's totally healed, and it's like nothing ever happened. Astrid asks if they've seen Colonel Broyles, and that he didn't come home the previous night.
In the morgue, Broyles contemplates his counterpart's corpse.
One of the Other Side's agents meets with the store owner and gives him an injection to restore his legs. The agent invites him to try out his legs, and the store owner gets up and discovers that he can walk. In return, the store owner gives the agent Bolivia's box as promised. Inside is the missing weapon component.
Peter is at Olivia's bedside when she wakes up. He apologizes, but Olivia explains that if it hadn't been for him, she never would have made it back. Peter kisses her tenderly on the forehead.